This is going to be short letter. There is the adage that one does not have a relationship with another in order to change them. In short, you should like them for who they are. Clichéd, yes but don't you think there is much truth in this?
Put Up with the Quirks
I can understand that the PERFECT match is rare, i.e. the sort of relationship you see in a two-hour "happily ever after" story. In the real world, there are lots of quirks that we wish our significant others did not have, but we put up with it because on balance it's worthwhile staying with that person despite the unnerving things they do.
My mother (that paragon of great relationship advice) says that a good relationship is all about give and take. What I think that means is that it's a compromise.
It's Criticism to Him
Is there a compromise here? It seems not. To me, it seems as if your beau has been quietly bearing up with all this criticism, because to him, despite your kind intentions, it's criticism. I've read and agree that the best communicators are those who could empathise with how others feel and say nothing.
Let Him Be Himself
If you really care about him, leave him alone to be himself and after a while (say a month) if there are a FEW things that REALLY upset you, TACTFULLY bring it up with him (so that you don't feel this is one-sided).
If that doesn't work, ask yourself whether you want to have a relationship with him. The choice is yours.